top of the rod(OP calls pin), flush with the top of the top clamp nut.

if you set it with the rod poking up too much, then you are trying to get the ball+brass into the neck portion of the sizer and its never gonna work, it will always jam.

lee dies (esp my 223 dies) want lube on the inside of the neck, I found that a tiny bit of lee lube inside every 3rd or 4th case keeps the expander from dragging on the neck at extraction. If it drags it will affect the case length.